Ward number 68, where the BJP has lost, is right opposite the Gorakhnath temple where Yogi Adityanath is head priest.
Independent candidate Nadira Khatoon has defeated the BJP's Maya Tripathi, her closest rival, by 422 votes.
"What can I say, I am really very happy . This is very overwhelming," said Ms Khatoon.
The news is bleak from three of four seats around the Gorakhnath temple. Two seats have gone to independents and one to the Samajwadi Party, which was decimated by the BJP in state polls eight months ago.
Yogi Adityanath has served as BJP lawmaker for 19 years in Gorakhnath, his adopted home town.
But the saffron-robed Chief Minister has enough to celebrate across India's most populous state, with 14 of 16 municipal corporations going to the BJP.
Ahead of the crucial Gujarat election this month, Yogi Adityanath and other BJP leaders have most to crow about in Amethi, the parliamentary constituency of Congress leader Rahul Gandhi. Commenting on the Congress drubbing in civic polls there, the Chief Minister said: "People who were saying big things about Gujarat, they haven't been able to open their account and have been cleared out of Amethi too."